6ELK | pdb_00006elk

C.elegans MnSOD-3 mutant - Q142H

PDB DOI: https://doi.org/10.2210/pdb6ELK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-09-29 Released: 2017-12-06
Deposition Author(s): Hunter, G.J., Trinh, C.H., Hunter, T.
Funding Organization(s): UoM

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.210 (Depositor), 0.215 (DCC)
R-Value Work:
0.183 (Depositor), 0.192 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A Single Mutation is Sufficient to Modify the Metal Selectivity and Specificity of a Eukaryotic Manganese Superoxide Dismutase to Encompass Iron.

Hunter, T., Bonetta, R., Sacco, A., Vella, M., Sultana, P.M., Trinh, C.H., Fadia, H.B.R., Borowski, T., Garcia-Fandino, R., Stockner, T., Hunter, G.J.

(2018) Chemistry 24: 5303-5308

PubMed: 29178484 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/chem.201704655
Primary Citation Related Structures:
6ELK

PubMed Abstract:
We have generated a site-directed mutant of the manganese superoxide dismutase SOD-3 of C.elegans (MnSOD-3) which modifies the metal specificity of the enzyme. While wild-type MnSOD-3 functions with manganese in the active site (3600 U mg ^-1 of protein) it has little or no activity when iron is incorporated. However, when histidine replaces glutamine 142 in the active site, the enzyme retains 50 % of its activity and becomes cambialistic for its metal cofactor exhibiting very similar specific activity with either manganese or iron.

Organizational Affiliation

Department of Physiology and Biochemistry, University of Malta, Msida, MSD2080, Malta.

Macromolecule Content

Total Structure Weight: 45.52 kDa
Atom Count: 3,513
Modeled Residue Count: 388
Deposited Residue Count: 390
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn] 2, mitochondrial	A, B [auth C]	195	Caenorhabditis elegans	Mutation(s): 1 Gene Names: sod-3, C08A9.1 EC: 1.15.1.1
UniProt
Find proteins for P41977 (Caenorhabditis elegans) Explore P41977 Go to UniProtKB: P41977
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41977
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C]	D [auth A] E [auth A] F [auth A] H [auth C] I [auth C] D [auth A], E [auth A], F [auth A], H [auth C], I [auth C], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth C] MOL2 format, chain C [auth A] MOL2 format, chain G [auth C] mmCIF format, chain C [auth A] mmCIF format, chain G [auth C]	C [auth A], G [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth C] Interactions & Density Focus chain C [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.210 (Depositor), 0.215 (DCC)
R-Value Work: 0.183 (Depositor), 0.192 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.53	α = 90
b = 81.53	β = 90
c = 137.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-06

Deposition Author(s):

Hunter, G.J.

Trinh, C.H.

Hunter, T.

Funding Organization	Location	Grant Number
UoM	Malta	MDS-BP

Revision History (Full details and data files)

Version 1.0: 2017-12-06
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description